16 papers · ranked by Valyu relevance
Daniel Deutsch, Rotem Dror, Dan Roth
There is significant interest in developing evaluation metrics which accurately estimate the quality of generated text without the aid of a human-written reference text, which can be time consuming and expensive to collect or entirely unavailable in online applications. However, in this work, we demonstrate that these…
Sung-Gwon Lee, Dokyun Na, Chungoo Park
Background Lately, high-throughput RNA sequencing has been extensively used to elucidate the transcriptome landscape and dynamics of cell types of different species. In particular, for most non-model organisms lacking complete reference genomes with high-quality annotation of genetic information, reference-free (RF) de…
Aureliana F. C. Chilengue, Daniel J. Whiley, Kate Cox, Maria Rosa Domingo-Sananes + 1 more
Whole-genome sequencing (WGS) of Mycobacterium tuberculosis (Mtb) is widely used in epidemiological investigations of recent transmission events, resulting in high-resolution strain typing. Accurate and rapid strain typing is essential for informing outbreak investigations and guiding tuberculosis control strategies.…
Subhankar Roy, Dilip Kumar Maity, Anirban Mukhopadhyay
Deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) sequence compressors for novel species frequently face challenges when processing wide-scale raw, FASTA, or multi-FASTA structured data. For years, molecular sequence databases have favored the widely used general-purpose Gzip and Zstd compressors. The absence of…
Phuong Vo, Yuehua Cui
Cell-type deconvolution has been instrumental for the analysis of spatial transcriptomics (ST) data to reveal underlying tissue heterogeneity. Although reference-based methods have been widely explored, practical limitations, particularly the need for matched single-cell RNA-seq data sets, highlight the value of robust…
Batuhan Eralp, Emre Sefer
Background Cancerous cells’ identity is determined via a mixture of multiple factors such as genomic variations, epigenetics, and the regulatory variations that are involved in transcription. The differences in transcriptome expression as well as abnormal structures in peptides determine phenotypical differences. Thus…
Tarachand Gupta, Rahul Madhavan, Xuchao Zhang, Chetan Bansal + 1 more
'Saravan Rajmohan'] We introduce REFA, a family of reference-free alignment methods that optimize over multiple user preferences while enforcing fine-grained length control. Our approach integrates deviation-based weighting to emphasize high-quality responses more strongly, length normalization to prevent trivial…
Thomas Dupic, Angela M. Phillips, Michael M. Desai
In a recent preprint, Park, Metzger, and Thornton reanalyze 20 empirical protein sequence-function landscapes using a “reference-free analysis” (RFA) method they recently developed. They argue that these empirical landscapes are simpler and less epistatic than earlier work suggested, and attribute the difference to…
Thomas Dupic, Angela M. Phillips, Michael M. Desai
In a recent preprint, Park, Metzger, and Thornton reanalyze 20 empirical protein sequence-function landscapes using a “reference-free analysis” (RFA) method they recently developed. They argue that these empirical landscapes are simpler and less epistatic than earlier work suggested, and attribute the difference to…
Xiaoxiao Shi, Jun Li, Tong Liu, Hanbo Zhao + 4 more
'Keping Sun' 'Jiang Feng' 'Shailender Kumar Verma'] Differences in gene expression within tissues can lead to differences in tissue function. Understanding the transcriptome of a species helps elucidate the molecular mechanisms underlying phenotypic divergence. According to the presence or absence of a reference genome…
S. K. Mukherjee
stress-free reference Authors: ['S. K. Mukherjee'] We often determine the constitutive relation for an initially stressed reference using the response of a virtual stress-free reference. However, it is usually difficult to identify the constitutive relation of the associated stressfree reference without conducting…
Nick Webster, Marco Servetto, Michael Homer
Existing minimal Object-Oriented models (OO), like Featherweight Java (FJ), are valuable for modelling programs and designing new programming languages and tools. However, their utility in developing realworld programs is limited. We introduce the 'Fearless Heart', a novel object calculus preserving FJ's minimal and…
Fa-Ting Hong, Xu Zhan, Haiyang Liu, Qinjie Lin + 5 more
'Zhixin Shu' 'Yang Zhou' 'Duygu Ceylan' 'Dan Xu'] Diffusion-based human animation aims to animate a human character based on a source human image as well as driving signals such as a sequence of poses. Leveraging the generative capacity of diffusion model, existing approaches are able to generate high-fidelity poses…
Varsha Achuthan, Deeptangi Mangsuli, Neelam Sinha, Shweta Ramdas
This paper introduces ”SVD-FCGR,” a scalable and efficient frame-work for phylogenetic analysis using Singular Value Decomposition (SVD) on Frequency Chaos Game Representation (FCGR). Unlike traditional MSA techniques, SVD-FCGR handles large datasets with lower computational complexity. It supports both genome-wide and…
Authors not listed
Finite-temperature lattice free energy differences between polymorphs of molecular crystals are fundamental to understanding and predicting the relative stability relationships underpinning polymorphism, yet are computationally expensive to obtain. Here, we implement and critically assess machine-learning-enabled…
Jingyao Chen, Aviva Borison, Douglas Densmore, Wilson W. Wong
Cell-free gene expression systems are increasingly important in fundamental research and biomanufacturing, offering a versatile platform for studying gene circuits and bio-computation. We present the Cell-Free Recombinase Integrated Boolean Output System (CRIBOS), a site-specific recombinase-based multiplex genetic…